© Inter-Research 2015, www.int-res.com. We studied the persistence of fishing impacts on coral reef fish assemblages by sampling 2 protected and 2 fished locations, using random replicate stereo baited remote underwater video. At each location we sampled a variety of coral reef habitats on 4 separate occasions between 2006 and 2007. We tested for consistency in differences in the biomass of target and nontarget species, trophic groups and overall assemblages. Generally, target species were more abundant and/or larger at protected locations. Many non-target species were either more abundant or depleted at protected sites, and some of these species were significantly larger or smaller. Trophic groups such as piscivores, piscivore invertivores, invertivores and planktivores were consistently more abundant within protected locations. Generally, greater numbers of species and individuals were found on protected reefs, though this was not consistent in all cases across all 4 sampling periods. These findings are consistent with the theory that protected areas can increase the abundance of not just target species but overall fish assemblages. These findings provide evidence for ecological mechanisms such as predator-prey interactions, competitive release, and benefits to invertivores, omnivores and other non-target groups from the presence of more abundant and larger target species within marine protected areas.